PROJECT SUMMARY The Germ-free and Gut Microbiology Core C is an essential component of this PPG competitive renewal application that will control for and quantify the modulating role of the gut flora in innate immunity during experimental IBD. The core will provide PPG investigators with: 1) germ-free (GF) ileitis-prone and ileitis-free mice, and 2) sequencing and culture-based analysis of the gut microbiota. Developing a core infrastructure to study the role of the gut flora in modulating experimental CD using a common centralized facility is crucial to the success of the Program, and represents a cost-effective alternative to guarantee proper and reproducible results. The core will provide a highly-controlled environment to differentiate strain-specific and strain-independent mechanisms of CD-associated innate immunity that may be modulated by the gut microbiota. To support the research strategies proposed in this PPG project and the research benefits of the unique pattern of intestinal disease present in the SAMP1/YitFc mouse model of CD-like ileitis, the Specific Aims of the Germ-free and Gut Microbiome Core C will be to: Aim 1). Conduct mechanistic microbiota studies in which human or mouse gut flora will be transplanted into GF mouse models of CD (SAMP or AKR) to quantify the modulatory role of the gut microbiome on innate immunity. This core will expand on our current knowledge and logistic infrastructure to provide mouse and human gut microbiota transplantation services into GF mice in order to test the hypotheses proposed in this PPG, while implementing new methods to accurately study the gut microbiota. Aim 2). Provide a culture-based microbiological service approach to identify microbial determinants of intestinal disease severity. This core will provide consultation and services to effectively identify cultivable microorganisms that could modulate intestinal disease severity. Beneficial/anti-inflammatory microbes will ultimately have the potential to become commercial probiotics. Aim 3). Provide cost-effective gut microbiome DNA and RNA-based sequencing analyses of samples from mice with or without genetic mutations as proposed in this grant. This core will centralize current in site and remote sequencing and analytical capabilities and unify protocols that we have validated with our collaborators to provide 16S rRNA microbiome analysis to the PPG projects. Established collaborations at CWRU and the Argonne National Laboratory at the University of Chicago will facilitate and standardize study design, sampling, and sequencing/data analysis protocols for microbiome and metatranscriptomic analysis.